Modern Human, Neanderthal, and Denisovan cross-breeding

I went to talk by David Reich, Harvard Med School, last Thursday on genetic evidence measuring interbreeding among modern humans, Neanderthals, and Denisovans. His talk also included significant background information.

First, he covered the techniques and difficulty of getting DNA samples from old bones. Typically, the body has been completely contaminated with bacteria, fungi, plants, and insects. Even after all their efforts at selecting protected interior portions of protected bones, less than 3% of the recovered DNA is mammalian. This also explains the early emphasis on mitochondrial DNA. There are thousands of mitochondria per copy of cell DNA. This makes it much easier to get an acceptable sample of mitochondrial DNA.

Then he explained significant differences between Neanderthals and Denisovans. For those who missed the recent news, the Denisovans are another form of human. Remains were found in the Denisovan caves in southern Siberia in 2010. Based on DNA clustering, the Denisovans, Neanderthals, and Modern Humans are each distinct. Within these three the various DNA samples cluster tightly and overlap in variations. There is a substantial and statistically significant separation between the three.

There are multiple samples of DNA for all these human variations. These are sufficient to obtain reasonably complete genomes, despite the limited samples.

Neanderthal range is Europe and to an unknown extent eastward into Central and Southern Asia. So far, the only Denisovan source is the caves in southern Siberia.

He then explained his terminology. When comparing different animals, like man vs chimpanzees, they look at gene overlap. When measuring interbreeding, they look at base-pair matching. The basic measure is to find single base-pair changes in a gene, then determine how often that change is found in Modern vs Neandertal vs Denisovan. This is used to derive percent sources.

Results:

Africans have the largest genetic diversity of modern humans and no measurable contribution of DNA from Neanderthal or Denisovan.

Non-Africans have about 2.5% Neanderthal DNA. This level is relatively uniform across all non-Africans.

There is a cluster of Denisovan contribution in Papua, New Guinea, Australia and neighboring islands. This level is not uniform. Outside this region there is no Denisovan contribution. Within these clusters there is one group at about 2.5% Denisovan, plus two other groups with different substitutions but both at about 5% Denisovan.

Based on change rates for base-pair substitutions, these interbreedings took place about 50K ya for both Neanderthals and Denisovans.

Speculations

The simplest explanation for the Neanderthal mix is the "out of Africa" theory, with the interbreeding taking place in the Levant. There is paleontological evidence for both Neanderthal and Modern humans living in the same hills at the same time, about 35-50K ya. This is consistent with migration from Africa. The lack of any Neanderthal contribution to Africans makes other mixing unlikely.

More speculatively, it also supports the hypothesis that the southern route (arabia, india, southeast asia, to australia) was first for modern human expansion. This would explain multiple interbreeding events with Denisovans that affect only southeast asia and australia. There was a second wave of modern humans from china later. This shows up in the genetics, and shows that this was a separate event from the earlier wave.

Unrelated Comment

There is increasing evidence that interbreeding events are the norm, not unusual. Genetics show events where Europeans substantially contributed to India. There is presently a major interbreeding event between Africans and Amerindians in south america. This is a change from previous theories that interbreeding events were rare.

Audience Questions:

What percent of interbreeding couples does this indicate? At most 2%, probably less than 1%, of children would be from interbreeding. The genetic match is close enough that this must have been a social effect, not a viability effect. There should have been no biological problems with interbreeding. If the percent was above 2% the overlap the genetic overlap would be higher.

What about the "hobbits" of Indonesia? No usable DNA could be recovered. Hot climates degrade DNA too fast. There are no usable DNA samples from any prehistoric bones of humans in hot climates.